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Re: [GUSDEV] Inserting Sequence Features - Problem with a big reference.
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From: Ricardo B. <rb...@gm...> - 2005-12-08 11:04:36
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Thanks Mark,
But now I have another error.
It follows below:
[rbalbi1@crithidia bancos]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
$GUS_HOME/config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt
--fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer
"2005-12-06" --commit
Thu Dec 8 09:04:53 2005 ARG algoinvo 1
Thu Dec 8 09:04:53 2005 ARG comment
Thu Dec 8 09:04:53 2005 ARG commit 1
Thu Dec 8 09:04:53 2005 ARG debug 0
Thu Dec 8 09:04:53 2005 ARG defaultOrganism
Thu Dec 8 09:04:53 2005 ARG extDbName Kinetoplastida_nt
Thu Dec 8 09:04:53 2005 ARG extDbRlsVer 2005-12-06
Thu Dec 8 09:04:53 2005 ARG fileFormat genbank
Thu Dec 8 09:04:53 2005 ARG gff2GroupTag
Thu Dec 8 09:04:53 2005 ARG group
Thu Dec 8 09:04:53 2005 ARG gusconfigfile
/GUS/gus_home/config/gus.config
Thu Dec 8 09:04:53 2005 ARG handlerExternalDbs
Thu Dec 8 09:04:53 2005 ARG help
Thu Dec 8 09:04:53 2005 ARG helpHTML
Thu Dec 8 09:04:53 2005 ARG inputFileExtension
Thu Dec 8 09:04:53 2005 ARG inputFileOrDir kinetoplastida_nt
Thu Dec 8 09:04:53 2005 ARG makeSourceids
Thu Dec 8 09:04:53 2005 ARG mapFile
/GUS/gus_home/config/genbank2gus.xml
Thu Dec 8 09:04:53 2005 ARG naSequenceSubclass
Thu Dec 8 09:04:53 2005 ARG project
Thu Dec 8 09:04:53 2005 ARG seqIdColumn source_id
Thu Dec 8 09:04:53 2005 ARG seqSoTerm
Thu Dec 8 09:04:53 2005 ARG seqType
Thu Dec 8 09:04:53 2005 ARG soCvsVersion
Thu Dec 8 09:04:53 2005 ARG sqlVerbose 0
Thu Dec 8 09:04:53 2005 ARG testNumber
Thu Dec 8 09:04:53 2005 ARG user
Thu Dec 8 09:04:53 2005 ARG verbose 0
Thu Dec 8 09:04:53 2005 ARG veryVerbose 0
Thu Dec 8 09:04:53 2005 AlgInvocationId 30
Thu Dec 8 09:04:53 2005 COMMIT commit on
Thu Dec 8 09:04:55 2005 Processing file 'kinetoplastida_nt'...
DBD::Pg::st execute failed: ERROR: cannot insert into a view
HINT: You need an unconditional ON INSERT DO INSTEAD rule.
ERROR:
SQL ERROR!! involving
Values: 4 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b=
0)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} Values: 4') called at
/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa90=
4b0)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY(0xa148314)') call=
ed
at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1813
GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1680
GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
731
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'Bio::Seq::RichSeq=3DHASH(0xb0aa2d8)', 4, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
330
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'HASH(0xabe05b0)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x9c82c20)',
'ARRAY(0x9c96700)') called at /GUS/gus_home/bin/ga line 11
STACK TRACE:
at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b=
0)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} Values: 4') called at
/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa90=
4b0)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY(0xa148314)') call=
ed
at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1813
GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1680
GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
731
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'Bio::Seq::RichSeq=3DHASH(0xb0aa2d8)', 4, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
330
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'HASH(0xabe05b0)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x9c82c20)',
'ARRAY(0x9c96700)') called at /GUS/gus_home/bin/ga line 11
Could you help me ?
thanks again,
Ricardo Balbi
2005/12/7, Mark S. Heiges <mh...@ug...>:
>
> One short term solution is to adjust your local schema "alter table
> SRes.Reference modify (author varchar2(4000))", or something like
> that, and then restart the loading.
>
> You can also file a feature request in the GUS Schema issue tracker
> to increase that column in a future release - https://
> www.cbil.upenn.edu/tracker.
>
> On Dec 6, 2005, at 6:48 PM, Ricardo Balbi wrote:
>
> > Hi,
> >
> > I am trying to load kinetoplastida_nt, using
> > InsertSequenceFeatures plugin. But I am not obtaining.
> > Kinetoplastida_nt has a register whose author field exceeds the
> > maximum size the table sres.reference.
> >
> > How I must proceed to load this base?
> >
> > It follows below the error:
> >
> > [rbalbi1@crithidia bancos]$ ga
> > GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/
> > config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt --
> > fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer
> > "2005-12-06" --commit
> > Tue Dec 6 21:32:42 2005 ARG algoinvo 1
> > Tue Dec 6 21:32:42 2005 ARG comment
> > Tue Dec 6 21:32:42 2005 ARG commit 1
> > Tue Dec 6 21:32:42 2005 ARG debug 0
> > Tue Dec 6 21:32:42 2005 ARG defaultOrganism
> > Tue Dec 6 21:32:42 2005 ARG extDbName
> > Kinetoplastida_nt
> > Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06
> > Tue Dec 6 21:32:42 2005 ARG fileFormat genbank
> > Tue Dec 6 21:32:42 2005 ARG gff2GroupTag
> > Tue Dec 6 21:32:42 2005 ARG group
> > Tue Dec 6 21:32:42 2005 ARG gusconfigfile /GUS/
> > gus_home/config/gus.config
> > Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs
> > Tue Dec 6 21:32:42 2005 ARG help
> > Tue Dec 6 21:32:42 2005 ARG helpHTML
> > Tue Dec 6 21:32:42 2005 ARG inputFileExtension
> > Tue Dec 6 21:32:42 2005 ARG inputFileOrDir
> > kinetoplastida_nt
> > Tue Dec 6 21:32:42 2005 ARG makeSourceids
> > Tue Dec 6 21:32:42 2005 ARG mapFile /GUS/gus_home/
> > config/genbank2gus.xml
> > Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass
> > Tue Dec 6 21:32:42 2005 ARG project
> > Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id
> > Tue Dec 6 21:32:42 2005 ARG seqSoTerm
> > Tue Dec 6 21:32:42 2005 ARG seqType
> > Tue Dec 6 21:32:42 2005 ARG soCvsVersion
> > Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0
> > Tue Dec 6 21:32:42 2005 ARG testNumber
> > Tue Dec 6 21:32:42 2005 ARG user
> > Tue Dec 6 21:32:42 2005 ARG verbose 0
> > Tue Dec 6 21:32:42 2005 ARG veryVerbose 0
> > Tue Dec 6 21:32:42 2005 AlgInvocationId 26
> > Tue Dec 6 21:32:42 2005 COMMIT commit on
> > Tue Dec 6 21:32:44 2005 Processing file 'kinetoplastida_nt'...
> > DBD::Pg::st execute failed: ERROR: value too long for type
> > character varying(1000)
> >
> > ERROR:
> >
> > SQL ERROR!! involving
> >
> > INSERT INTO SRes.Reference ( journal_or_book_name,
> > group_write, other_read, group_read, author, user_read,
> > row_user_id, reference_id, modification_date, other_write,
> > row_alg_invocation_id, row_project_id, row_group_id, title,
> > user_write )
> > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? )
> > Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1,
> > 1, 1, El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D.,
> > Aggarwal,G., Tran,A.N., Ghedin,E., Worthey,E.A., Delcher,A.L.,
> > Blandin,G., Westenberger,S.J., Caler,E., Cerqueira,G.C.,
> > Branche,C., Haas,B., Anupama,A., Arner,E., Aslund,L., Attipoe,P.,
> > Bontempi,E., Bringaud,F., Burton,P., Cadag,E., Campbell,D.A.,
> > Carrington,M., Crabtree,J., Darban,H., da Silveira,J.F., de
> > Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T.,
> > Ferella,M., Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y.,
> > Kindlund,E., Klingbeil,M., Kluge,S., Koo,H., Lacerda,D.,
> > Levin,M.J., Lorenzi,H., Louie,T., Machado,C.R., McCulloch,R.,
> > McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S.,
> > Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M.,
> > Ramirez,J.L., Rinta,J., Robertson,L., Salzberg,S.L., Sanchez,D.O.,
> > Seyler,A., Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T.,
> > Tarleton,R., Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N.,
> > Wickstead,B., Wortman,J., White,O., Fraser,C.M., Stuart,K.D. and
> > Andersson,B., 1, 1, 6, 0, 26, 1, 1, The genome sequence of
> > Trypanosoma cruzi, etiologic agent of Chagas disease, 1 at /GUS/
> > gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
> > GUS::ObjRelP::DbiDbHandle::death
> > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d14)', '\x{a} SQL ERROR!!
> > involving\x{a} \x{a} INSERT INTO SRes.Reference ( j...') called
> > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
> > GUS::ObjRelP::DbiDbHandle::sqlExec
> > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d14)',
> > 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x8e826cc)', 'ARRAY
> > (0x8e82708)', '\x{a} INSERT INTO SRes.Reference
> > ( journal_or_book_name, grou...') called at /GUS/gus_home/lib/perl/
> > GUS/ObjRelP/DbiRow.pm line 666
> > GUS::ObjRelP::DbiRow::quote_and_insert
> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)', 'HASH(0x9889d48)')
> > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
> > GUS::ObjRelP::DbiRow::insert
> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)') called at /GUS/
> > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
> >
> >
> > thanks,
> > Ricardo
>
>
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